Currently, I have the composition at 29.95fps with different animation effects applied. When I change the fps to 25fps, a weird thing happened - a section of a layer that had puppet tool animation disappeared.

What are you expected to DELIVER? 25 or 29.97? That is what will determine the frame rate.

So how do you convert the footage to the necessary frame rate? There are a number of ways to do it, and since we have no details about your system nor the software on it, it's extremely difficult to tell you what to do. It would also help to know if this frame rate conversion has to look professional, or if it's just going to end up on YouTube.

[Chin Park]"...a section of a layer that had puppet tool animation disappeared...."

Yeah, that'll happen when you don't choose a frame rate and stick with it. You sort of put the cart before the horse. Sorry.

It will most likely be for HD TV. I have Adobe Master CS4 on a Windows Vista. Let me know if there is any other information you need.

And I was also wondering if there were general rules to follow:
- Is exporting at higher frame rate better even if some of the footages have less?
- If I export at 25fps, is it still better to set up the composition at 29.97fps?

Hi, if you footage have 25 fps and you put it in a 29,97 fps comp the video is going to run faster than the original so you have to modify the speed of the layer to make it correct.
I recomend that if you have to deliver the final work in 29.97 fps first of all convert all your footage to that fps and work with all your material, comps and exports on the same rate...
I hope this help you...

Before I read your reply, I thought that footages with lower fps duplicate some frames to match the timing. If speeding up of footage is the only outcome of mismatching fps, then it will not be a big deal in this project I'm working on.

So does interpreting the footage in After Effects to different fps count as converting?

But dude, you didn't answer the essential question that I asked right away -- WHATFRAMERATEDOYOUNEEDTODELIVER? You can't mix frame rates without courting disaster, as you've already found out!

[Chin Park]"- Is exporting at higher frame rate better even if some of the footages have less?
- If I export at 25fps, is it still better to set up the composition at 29.97fps?"

The Frame Rates have to match! Get 'em to match!

[Chin Park]"It will most likely be for HDTV."

Okay, what resolution? 1920x1080 or 1280x720?
Are you making a videotape master for broadcast?
Do you have to FTP a file in a certain codec to meet spec?
Are you making DVD's or Blu-Rays?
Are you just posing this on Vimeo or YouTube?
Are you doing a project for Mrs. Filbert's summer remedial Intermediate Multimedia Production class at Hoover High?

I'm not sure about required fps yet. So when I find out, I'll make sure all the assets match. What do you do for instances when the client does not know or they will be doing the final preparations?

I am delivering in Quicktime movie with animation codec at 1920 x 1080, progressive. It may be for broadcast. I want to deliver in highest quality and also make it most convinient for client to make conversions for broadcast, if they decide to.

[Chin Park]"What do you do for instances when the client does not know or they will be doing the final preparations? "

Thank you VERY MUCH for revealing what's going on. You see? You didn't betray any confidences. I thought you were a clueless high school kid for a moment.

In your situation, I would wait until the client makes up his/her flippin' mind on the delivery specifications. But we are talking about being professional, communicating with a client to make sure things are done right the first time, and courtesy is a must.

I politely inform him/her that work on the project cannot begin until the delivery specifications are well-established. Such information is too fundamental to the project to ignore. Otherwise, I will be forced to make both 25fps and 29.97 fps versions, which will of course mean that you, Mr./Mrs. Client, will be charged more. This is something which I definitely wish to avoid by making the delivery specifications clear from the start.

Sound diplomatic enough? Clear specs need to be established, and established RIGHT NOW to avoid inefficiency, duplicated work, and unnecessary charges to the client.

Right now your hands are tied with these conflicting frame rates. Somebody's got to make a decision, and that somebody is the client.

Actually what you can do is first create the project in 29.97 fps 1080p, then if you need 25 fps, create a new composition with that framerate, and drag the 29.97 fps comp into it. The new comp can pull interframe data from the 29.97 fps project, and it will be as if it was created in 25 fps. This works perfectly with graphics created in After Effects, though can get a little tricky when working with pre-rendered footage (there may be some frame blending if you enable it).

I agree with the frame blending, it does not look good, which is why it should be disabled.

However, the animation is smooth when the 29.97 comp is placed in the 25 fps comp. As I said, it appears After Effects can pull inter-frame data from the 29.97 comp. What this means is that it will not render in 29.97, then convert to 25 fps, but instead will render the animation at true 25 fps. Sure, your keyframes won't line up exactly with a frame in the 25 fps comp, but this shouldn't make any noticeable changes to it visually.